J. Bio. Env. Sci.

2016

Journal of Biodiversity and Environmental Sciences (JBES)

ISSN: 2220-6663 (Print) 2222-3045 (Online)
Vol. 8, No. 4, p. 221-230, 2016
http://www.innspub.net

RESEARCH PAPER OPEN ACCESS

Prokaryotic community profiles of soils from Mayon volcano,

Philippines based on 16S ribosomal RNA gene sequences

Kristel Mae DL. Perdigon, Asuncion K. Raymundo, Rina B. Opulencia*

Microbiology Division, University of the Philippines Los Baños, College, Laguna, Philippines
Article published on April28, 2016

Key words: 16S rRNA gene, Bacteria, Archaea, Mayon Volcano, Diversity.

Abstract
Mayon Volcano is the Philippines’ most active volcano. Despite extensive pedological, ecological and
ethnobotanical studies, no published information is known about its soil microflora. In this study, to determine
the microbial community profiles, 16S rRNA gene was amplified and sequenced from genomic DNA isolated from
volcanic soils collected from altitudinal gradients of Mayon Volcano. Phylogenetic analyses revealed 10 bacterial
phyla, including an unclassified group, with Acidobacteria (40.6%) as the most dominant phylum. Archaea were
distributed into three phyla and an unclassified archaeal group (53.9%), which comprised the majority. The
composition of the prokaryotic community suggests roles in the cycling of organic and inorganic nutrients in
Mayon Volcano ecosystem. At p<0.1, soil pH and organic matter content showed significant correlation with
species richness of Archaea and diversity of Bacteria. In contrast, altitude, soil temperature and soil moisture
content showed no significant influence on the composition and distribution of microorganisms in Mayon
Volcano. This study provides the first known information on the prokaryotic composition of Mayon Volcano,
including the soil properties that influence the structuring of these communities.
*CorrespondingAuthor:Rina B. Opulenciarbopulencia@up.edu.ph

221 | Perdigonet al.


Introduction
Mayon Volcano, also known as Mount Mayon, is a
perfect stratovolcano rising to 2,462 m in the
province of Albay on the island of Luzon in the
Philippines. Its almost symmetric conical shape is
famous world-wide. Mayon Volcano is the most active
volcano in the country, registering over 50 eruptions
over four centuries. Despite extensive pedological
(Aberin, 2004), ecological (Dayao, 1994), and
ethnobotanical studies (Buot et al., 2009) conducted
in and around Mayon Volcano, there is a dearth of
information on the microbiological diversity of its
soil.
The prokaryotes, which are distributed into domains
Bacteria and Archaea, are ubiquitous, comprising the
majority of organic matter on earth (Whitman et al.,
1998). They exhibit great metabolic and genetic
diversity, and are major environmental determinants,
responsible for the cycling of organic and inorganic
compounds. They can also influence above-ground
ecosystems by contributing to plant nutrition, plant
health, soil structure, and soil fertility (Kirk et al.,
2004). Microbial biomass in soil and their activities
are frequently used as an early indicator of changes in
soil chemical and physical properties resulting from
soil management and environmental stresses (Trasar-
Cepeda et al., 1998). Several environmental factors
such as carbon and energy sources, available water,
temperature, and pH can affect the ecology, activity
and population dynamics of microorganisms in soil
(Nannipieri et al., 2003).
This study aims to determine the bacterial and
archaeal community profiles in soils of Mayon
Volcano. The information on the number of species of
microorganisms, and their respective phylogenetic
distribution, can lead to understanding the pattern
and tempo of microbial diversification, as well as the
complexity of this ecosystem. In addition, species-rich
phylogenies may find practical application in
ecosystem management, agriculture, drug discovery
and medicine (McLaughlin et al., 2009). The study
also aims to correlate soil parameters such as
222 | Perdigonet al.
J. Bio. Env. Sci. 2016
temperature, pH, organic matter, moisture content,
and altitude with the diversity of prokaryotes, to gain
insight on the abiotic factors that may influence the
assembly of these microbial communities in Mayon
Volcano.
Materials and methods
Volcanic soil sample collection
Soil samples were collected from 500 meters above
sea level (m asl), 1000 m asl, and 1500 m asl of
Mayon Volcano. Elevation and coordinates of the
study sites were determined using a Global
Positioning System tracker (Garmin, USA). Each
sampling site was 20 m away from the main trail.
Within each site, three areas, 10 m away from each
other, were measured and marked. In each of the
three areas, soil samples were collected in 10 different
points at 10 cm depth. Collection points were 1 m
apart in a zigzag manner. Collected soil samples per
elevation were mixed using trowel and pail from
which three sterile bags of soil were obtained as
replicates. During transport, the soil samples were
kept at room temperature but kept at 4°C in the
laboratory until testing. Representative samples for
DNA extraction were stored at below 20°C.
Physico-chemical parameters of volcanic soils
Volcanic soil samples were submitted for analysis of
organic matter (OM) content to the Analytical
Services Laboratory, Soils and Agro-Ecosystem
Division of Agricultural Systems Cluster, College of
Agriculture, University of the Philippines Los Baños.
Environmental soil temperature was measured using
a thermometer during the time of collection.The pH
of the soil mixture was determined using Milwaukee
pH600 pocket-sized pH pen (Milwaukee
Instruments, USA). To measure the moisture content
of the soil, samples were placed on pre-weighed petri
plate, dried in 50°C oven, and weighed every other
day until the soil had dried to a constant weight.
Extraction of total genomic DNA
The total genomic DNA was extracted from each soil
sample by using the FastDNA® SPIN Kit for Soil (MP

Biomedicals, LLC, Illkrich, France) by following the
manufacturer’s protocol. However, 20 mg of skim
milk were added to the Lysing Matrix E tube with the
soil sample.
Amplification of prokaryotic 16S rRNA Gene by
polymerase chain reaction (PCR)
Bacteria
Amplification of bacterial 16S rRNA gene was
performed in a 50 μL reaction mixture containing 1X
KAPA HiFi buffer, 0.3 mM dNTPs, 0.3 µM of each of
primers 27F (AGAGTTTGATCMTGG CTCAG) (Lane,
1991) and 1492R (GGGTTACCTTG TTACGACTT)
(Stackebrandt and Liesack,1993), 1 U KAPA HiFi
HotStart DNA polymerase, and 4.0 μL of template
DNA. The thermal cycling program was run on
GeneTest PCR machine (Bio-Gener Technology,
China) as follows: 5 min of initial denaturation at
95°C; 35 cycles of 20 sec denaturation at 95°C; 20 sec
annealing at 57°C; 1 min and 30 sec extension at
72°C; and 5 min final extension at 72°C with holding
temperature of 4°C.
Archaea
Amplification of archaeal 16S rRNA gene was
performed in 25 uL of PCR reaction mix containing
1X Q5 Reaction Buffer, 0.2 mM dNTPs, 0.5 µM each
of primers 21F (TTCCGGTTGATCCYGCCGGA where
Y= C or T) (DeLong, 1992) and 1391R
(GACGGGCGGTGTGTRCA) (Barns et al., 1994;
Reysenbach et al., 1994), 1X Q5 enhancer, 0.5 U Q5®
High Fidelity DNA polymerase, and 4.0 μL template
DNA. The thermal cycling program was run on
GeneTest PCR machine (Bio-Gener Technology,
China) as follows: 1 min initial denaturation at 98°C,
35 cycles of 10 sec denaturation at 98°C, 20 sec
annealing at 62°C, 1 min extension at 72°C, and 5
min final extension at 72°C with holding temperature
of 4°C.
Purification of PCR amplicons
Amplification products were purified by using the
QIAquick PCR Purification Kit (QIAGEN Inc.,
California, USA), following the manufacturer’s
223 | Perdigonet al.
J. Bio. Env. Sci. 2016
instructions.
Construction of prokaryotic 16S rRNA gene libraries
Purified 16S rRNA genes of Bacteria and Archaea
were each cloned into pENTR™/D-TOPO® vector
(Invitrogen, Life Technologies, California, USA). A
ligation mixture containing 0.2 mM salt solution, 10
ng of purified 16S rRNA gene, and 20 ng of vector was
gently mixed and incubated at 23˚C in the thermal
cycler for 15 min. Two microliters of the ligation
mixture were added into tube containing freshly
thawed E. coli DH5α cells, which were then allowed to
stand on ice for 20 min. Cells were heat-shocked by
incubating the tubes at 42˚C water bath for 90 sec,
and immediately incubated back on ice for 3 min. To
permit growth of cells, 950 μL of SOC medium were
added to tubes, which were incubated at 37˚C with
shaking at 30 x g for 1 h. One hundred microliters of
the SOC medium were plated on SOB plates with 50
μg/mL kanamycin. The remaining 900 μL SOC
medium were pelleted by centrifugation at 665 x g for
3 min, which were then plated on SOB medium with
50 μg/mL kanamycin. All plates were incubated
overnight at 37˚C.
Analysis of transformants by PCR
Transformants on SOB plates with kanamycin were
individually picked and resuspended into 20 μL PCR
mix containing 1X PCR buffer, 0.25 mM dNTPs, 0.2
uM of each of primers M13F and M13R (Thermo
Fisher Scientific, California, USA), 3.0% DMSO, and 1
U Taq polymerase. The thermal cycling program was
run on GeneTest PCR machine (Bio-Gener
Technology, China) as follows: 5 min initial
denaturation at 94˚C, 35 cycles of 30 sec
denaturation at 94˚C, 30 sec annealing at 57˚C, 1 min
and 30 sec extension at 72˚C, and 7 min final
extension at 72˚C with holding temperature of 4˚C.
Transformants showing the expected size of the
amplified insert on agarose gel electrophoresis were
selected and inoculated to LB broth tubes with
kanamycin for plasmid isolation. The tubes were
incubated overnight with shaking at 37˚C.
 J. Bio. Env. Sci. 2016

Isolation of plasmid DNA putative clones 90, 92, 94 or 97%, respectively (Desantis et al., 2007).
Plasmids bearing correct insets were isolated using ClustalW software was used for multiple sequence
the Perfectprep® Plasmid Midi Kit (Eppendorf, alignment. Phylogenetic trees were inferred using
California) by following the manufacturer’s protocol. neighbor-joining (NJ) tree algorithms (Saitou and
Nei, 1987) performed in MEGA 6 software (Tamura et
Analysis of DNA and measurement of DNA al., 2013). The robustness of the tree was evaluated by
concentration bootstrap analyses based on 1,000 reiterations.
The presence and purity of DNA were verified on a
1.5% agarose gel run at 90 V for 1 h in 0.5x Tris- Statistical analysis
acetate-EDTA (TAE) buffer (20 mM Tris, 10 mM The Kruskal-Wallis test was performed to determine
acetate, 0.5 mM EDTA, pH 8.0). The gel was stained significant differences in the physicochemical
with 0.5X GoodviewTM nucleic acid stain (SBS parameters of the soil samples. Phylogenetic data
Genetech Co., Ltd, China). DNA concentrations were were analyzed using the vegan package in R
estimated using NanoDropTM 8000 softwareversion 3.1.1 to measure Shannon index to
Spectrophotometer (Thermo Scientific, USA). estimate diversity (Hill et al., 2003) and species
richness. Analysis of variance was performed to
Analysis of DNA sequence determine the correlation between fungal diversity
Plasmids were sent to 1st Base DNA Sequencing (Shannon diversity) or species richness and
Services, Malaysia for sequencing. Obtained physicochemical properties of the soil.
sequences were manually evaluated using
ChromasPro version 2 software to remove the low Results and discussion
quality regions at both ends of the fragment. The Physicochemical parameters of soils
sequences obtained were compared to references in Soils from all sampled altitudes of Mayon Volcano
the BLAST Database server of the National Centre were acidic and statistically varied in moisture
for Biotechnology Information, allowing either content. The soil at 1500 m asl, the closest to the
specific phylogenetic classification or proposal of crater, was significantly most acidic, and contained
novel taxa when a clone is sufficiently divergent from the least moisture and least organic matter (Table 1).
known groups. Typically, cloned sequences were The organic contents of soil at lower altitudes were
assigned to phylum, class, order, family, subfamily or significantly higher than at higher altitude.
species at sequence similarity cut-off values of 80, 85,

Table 1. Physicochemical parameters of soil along altitudinal gradients of Mayon Volcano.

Altitude (m asl) Temperature (˚C) pH Moisture content Organic matter
(%) content (%)
500 26.33 ± 0.58A 5.93 ± 0.06A 56.44 ±2.46A 4.26 ± 0.32A
1000 22.33 ± 0.58B 5.53 ± 0.12A 40.34 ±1.15B 3.32 ± 0.83A
1500 22.00 ± 0.00B 4.10 ± 0.36B 14.47 ±2.27C 0.35 ± 0.13B
p-value = 0.05. Values within a column with the same letter are not significantly different.

Analysis of bacterial 16S rRNA gene sequences
Twenty-four molecular operational taxonomic units
(MOTUs) were generated from analysis of 16S rRNA
gene sequences of a library of 64 bacterial clones.
Majority of the bacterial population is represented by
the phylum Acidobacteria (Table 2). This phylum has
been consistently present in soils, comprising an
average of 20% of the global soil bacteria (Janssen,
2006; Barns et al., 2007). The abundance of these
bacteria in soils indicates their crucial roles in the

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 J. Bio. Env. Sci. 2016

sustainability of this ecosystem. Recent physiological bacterial community in Mayon Volcano appears
characterization of representative species within this similar to that of Changbai Mountain in China (Shen
phylum revealed that Acidobacteria can contribute to et al., 2013) and Atlantic Rainforest in Brazil (Lima-
global hydrogen cycling (Greening et al., 2015) and to Perim et al., 2016). Interestingly, Mount Fuji in
carbon cycling in forests (García-Fraile et al., 2015; Japan, also an active volcano, harbors similar
Lladóet al., 2015). It is likely that the Acidobacteria bacterial profile, except for Firmicutes,
enumerated in this study contribute to the cycling of Planctomycetes, and Armatimonadetes (Singh et al.,
nutrients in Mayon Volcano ecosystem. The profile of 2012).

Table 2. BLAST search results of the molecular operational taxonomic units (MOTU) of bacterial 16S rRNA gene
sequences from soils of Mayon Volcano.
MOTU Phylum BLAST search result Accession number Identity (%) Number of isolates at Frequency (%)
altitude (m asl)
500 1000 1500
1 Acidobacteria Holophaga foetida NR 036891.1 97 - - 1 1.6
2 Thermoanaerobaculum aquaticum NR 109681.1 100 - 2 - 3.1
3 Candidatus Koribacter versatilis NR 074350.1 100 9 - - 14.1
4 Acidobacterium capsulatum NR 043386.1 99 - 1 - 1.6
5 Granulicella paludicola NR 115072.1 98 2 - - 3.1
6 Candidatus Solibacter usitatus NR 074351.1 97 - 5 - 7.8
7 Blastocatella fastidiosa NR 118350.1 97 4 2 - 9.4
40.6
8 Firmicutes Bacillus acidiceler KF150386.1 98 1 - - 1.6
9 Paenibacillus contaminans NR 044325.1 98 3 - - 4.7
10 Streptococcus thermophilus NR 074827.1 97 2 2 2 9.4
15.6

Table 2 continued.
11 α-Proteobacteria Rhodobacter azotoformans NR 113300.1 97 - - 1 1.6
12 Mesorhizobium chacoense NR 025411.1 98 - - 1 1.6
3.1
13 β-Proteobacteria Massilia kyonggiensis NR 126273.1 97 1 - - 1.6
14 γ-Proteobacteria Arenimonas malthae NR 043670.1 97 - 1 - 1.6
15 Thermomonas brevis NR 025578.1 97 - 3 - 4.7
16 Lysobacter ginsengisoli NR 112563.1 99 - 2 - 3.1
9.4
17 δ-Proteobacteria Haliangium ochraceum NR 074917.1 100 1 - - 1.6
18 Planctomycetes Zavarzinella formosa NR 042465.1 98 1 - 1 3.1
19 Armatimonadetes Fimbriimonas ginsengisoli NR 121726.1 99 - - 1 1.6
20 Bacteriodetes Empedobacter haloabium strain NR 125708.1 97 2 1 - 4.7
21 Actinobacteria Ferrimicrobium acidiphilum NR 041798.1 99 1 - - 1.6
22 Acidothermus cellulolyticus NR 114693.1 99 1 - - 1.6
3.1
23 Unclassified Uncultured bacterium LN572827.1 95 2 4 - 9.4
24 Uncultured bacterium clone GQ247079.1 96 - - 4 6.3
15.6
Note: Numbers in boldface represent the total frequency per phylum.

Analysis of archaeal 16S rRNA gene sequences 2016). The significance of this dominant group of
Analysis of the 16S rRNA gene sequences of a library Archaea in these environments remains unknown but
of 26 archaeal clones revealed nine MOTUs. Majority their consistent presence in soil indicates important
of the clones (53.8%) belonged to the unclassified physiological role in this environment. Members of
group of Archaea (Table 3) as seen in soils of the other archaeal phyla, namely, Crenarchaeotea,
Atlantic Rainforest in Brazil (Lima-Perim et al., Thaumarchaeota, and Euryarchaeota, had also been

225 | Perdigonet al.

 J. Bio. Env. Sci. 2016

detected in soils of Mayon Volcano.These Archaea, are also likely involved in nitrate leaching from soils,
especially the ammonia-oxidizing archaea (AOA) in resulting to nitrogen loss from ecosystems and cause
the phylum Thaumarchaeota, have been surface and groundwater contamination. Moreover,
demonstrated to play major roles in global the activity of AOA may be a significant source of
biogeochemical cycles of nitrogen (Francis et al., greenhouse gas (nitrous oxide) emissions from the
2007) and carbon elements (Zhang et al., 2015). AOA soil (Kowalchuk and Stephen, 2001).

Table 3. BLAST search results of the molecular operational taxonomic units (MOTU) of archaeal 16S rRNA gene
sequences from soils of Mayon Volcano.
MOTU Phylum BLAST search result Identity Accession Number of isolates at altitude (m asl) Frequency (%)
(%) number
500 1000 1500
Crenarchaeota Uncult. crenararchaeote 97 EU306968.1 - 2 3 19.2
1 ArcB cF03
2 Thaumarchaeota Candidatus Nitrosopumilus 98 NR 102904.1 - 2 1 11.5
koreensis
3 Candidatus Nitrosophaera 99 NR 102916.1 - - 1 3.8
gargensis
15.4
4 Euryarchaeota Methanomassiliicoccus 99 NR 118098.1 2 1 - 11.5
luminyensis
5 Unclassified Uncult. Archaeon clone 96 FJ936629.1 3 - - 11.5
kaa66
6 Uncult. Arcceon lone Arc- 96 FJ584331.1 - 1 - 3.8
CS39
7 Uncult. Archaeon clone D92 97 FJ174726.1 3 2 - 19.2
8 Uncult. Archaeon YL-S-A 97 KC841495.1 1 1 - 7.7
9 Uncult. Archaeon Clone A 96 GU127873.1 1 2 - 11.5
P3K3f
53.8
Note: Numbers in bold represent the total percentage per phylum.

Table 4. Relationship of environmental parameters to Shannon diversity index and species richness of Bacteria
in Mayon Volcano.
Environmentalparameter Shannon diversity index Species richness
p-value r2 p-value
r2
Altitude 0.08 0.21 0.05 0.29
Soil Temp 0.76 0.54 0.72 0.62
pH 0.02 0.01*(0.77) 0.11 0.09*(0.09)
Moisture Content 0.14 0.16 0.05 0.24
Organic Matter Content 0.02 0.02*(36.7) 0.02 0.10
p-value = 0.1; * Environmental parameter with significant effect on Shannon diversity index and/or species
richness. Number after the asterisk (*) represents the magnitude of the effect.

Relationship between physicochemical properties of on the composition and distribution of prokaryotic

soil and microbial community community. Studies on the influence of soil edaphic
In Mayon Volcano, the pH of soil significantly (p<0.1) properties on the composition of microbial
affected the prokaryotic species richness and bacterial communities in the Atlantic Rainforest (Santos et al.,
diversity (Tables 4 and 5). The organic matter content 2014) and Sonoran Desert (Andrew et al., 2012)
of soil also influenced bacterial diversity as well as underline pH and organic matter concentrations as
species richness of Archaea. In contrast, altitude, soil among the main soil properties influencing microbial
temperature, and soil moisture content had no effect community composition and diversity in these soils.

226 | Perdigonet al.

 J. Bio. Env. Sci. 2016

Soil pH has been commonly correlated
variations in bacterial and archaeal communities
(Nicol et al., 2008; Faoro et al., 2010), and often the
best predictor of diversity and composition of
Bacteria (Fierer and Jackson, 2006; Tripathi et al.,
2012) and Archaea (Bengtson et al., 2012; Tripathi et
al., 2013).
The null effect of altitude on prokaryotic diversity and
species richness in Mayon Volcano were consistent
with with the findings of Fierer et al. (2011) on organic
soil, mineral soil, and leaf surface but in contrast with
those of Siles et al. (2016) where higher altitudes
resulted to significant increase in microbial
abundance, and Zhang et al. (2009) where altitude
and abundance of ammonia oxidizing archaea in Mt
Everest showed significant negative correlation. The
effect of altitude is not independent, being influenced
by other factors such as availability of soil organic
matter (Siles et al., 2016).

Table 5. Relationship of environmental parameters to Shannon diversity index and species richness of Archaea
in Mayon Volcano.
Environmentalparameter Shannon diversity index Species richness
r2 p-value r2 p-value
Altitude 0.49 0.34 0.04 0.28
Soil Temp 0.51 0.67 0.50 0.62
pH 0.98 0.14 0.05 0.08*(0.06)
Moisture Content 0.62 0.29 0.03 0.23
Organic MatterContent 0.06 0.15 0.01 0.09*(2.9)
p-value = 0.1; *Environmental parameter with significant effect in Shannon diversity index and /or Species
Richness; value after the asterisk (*) represents the magnitude of the effect.

Despite significant differences in moisture content in soil temperature and soil moisture content have no
soil from various site, surprisingly, soil moisture did effect on the composition and distribution of
not affect prokaryotic diversity and richness. microorganisms in Mayon Volcano.

These results are in contrast to several reports Acknowledgment

where moisture was the most significant predictor This work was funded by the Basic Research Program
of bacterial diversity at the genus level (Geyer et al., of the University of the Philippines Los Baños
2014) and one of the key factors in shaping soil awarded to RB Opulencia and partly by the Professor
microbiome (Crits-Christoph et al., 2013). Soil Emeritus grant of AK Raymundo. The Department of
temperature also showed no significant effect on the Science and Technology- Science Education
microbial composition of Mayon Volcano. Institute’s Accelerated Science and Technology
Human Resource Development Program (ASTHRDP)
Conclusion scholarship awarded to KMDL Perdigon supported
The bacteria in soils of Mayon Volcanoare distributed her graduate studies that allowed her to work on this
into 10 known phyla and an unclassified group, and project.
dominated by Acidobacteria while the Archaea were
represented by three phyla and an unclassified References
archaeal group, which comprises the majority. Soil Aberin VG. 2004. Pedological Characterizations of
pH and organic matter content are important factors Soils in Mount Mayon, Albay, Philippines
that influence the diversity and richness of the (Unpublished MSc thesis). University of the
prokaryotes in Mayon Volcano. However, altitude, Philippines Los Baños, Laguna, Philippines.

227 | Perdigonet al.

 J. Bio. Env. Sci. 2016

Andrew DR, Fitak RR, Munguia-Vega A, Desantis TZ, Brodie EL, Moberg JP, Zubieta
Racolta A, Martinson VG, Dontsova K. 2012. IX, Piceno YM, Andersen GL. 2007. High-density
Abiotic factors shape microbial diversity in Sonoran universal 16S rRNA microarray analysis reveals
Desert soils. Applied and Environmental broader diversity than typical clone library when
Microbiology 78, 217527-7537. sampling the environment. Microbial Ecology 53,
371–383.
Barns SM, Fundyga RE, Jeffries MW,Pace NR.
1994. Remarkable archaeal diversity detected in a Faoro H, Alves AC, Souza EM, Rigo LU, Cruz
Yellowstone National Park hot-spring LM, Al-Janabi SM, Monteiro RA, Baura
environment. Proceedings of the National Academy of VA,Pedrosa FO. 2010. Influence of soil
Sciences 91, 1609–1613. characteristics on the diversity of bacteria in the
Southern Brazilian Atlantic Forest. Applied and
Barns SM, Cain EC, Sommerville L, Kuske CR. Environmental Microbiology 76, 4744–4749.
2007.Acidobacteria Phylum sequences in uranium-
contaminated subsurface sediments greatly expand Fierer N, Jackson RB. 2006. The diversity and
the known diversity within the phylum. Applied and biogeography of soil bacterial
Environmental Microbiology 73, 3113-3116. communities. Proceedings of National Academy
Sciences 103, 626–631.
Bengtson P, Sterngren AE, Rousk J. 2012.
Archaeal abundance across a pH gradient in an arable Fierer N, Mccain CM, Meir P, Zimmermann
soil and its relationship to bacterial and fungal growth M, Rapp JM, Silman MR, Knight R. 2011.
rates. Applied and Environmental Microbiology 78, Microbes do not follow the elevational diversity
5906–5911. patterns of plants and animals. Ecology 92, 797-804.

Buot IE Jr. 2009. An ethnobotanical study of the Francis CA, Beman JM, Kuypers MM. 2007.
plant biodiversity of Mt. Mayon, BicolPeninsula, New processes and players in the nitrogen cycle: the
Albay, Philippines. Journal of Nature Studies 8, 1-10. microbial ecology of anaerobic and archaeal ammonia
oxidation. International Society for Microbial Ecology
Crits-Christoph A, Robinson CK, Barnum Journal 1, 19-27.
T, Fricke WF, Davila AF, Jedynak B, McKay
CP,Diruggiero J. 2013. Colonization patterns of soil García-Fraile P, Benada O, Cajthaml
microbial communities in the Atacama Desert. T, Baldrian P, Lladó S. 2015. Terracidiphilus
Microbiome 1, 28. gabretensis gen. nov., sp. nov., an abundant and
active forest soil Acidobacterium important in organic
Dayao AE. 1994. Morphostructure and hazard matter transformation. Applied and Environmental
implication in Mount Mayon Philippines: A GIS- Microbiology 82, 560-569.
assisted volcanic study hazards study (Unpublished
MSci thesis). University of the Philippines Los Baños,
Laguna, Philippines. Geyer KM, Altrichter AE, Takacs-Vesbach
CD, Van Horn DJ, Gooseff MN, Barrett JE.
DeLong EF. 1992. Archaea in coastal marine 2014. Bacterial community composition of divergent
environments. Proceedings of the National Academy soil habitats in a polar desert. Federation of
of Sciences, 89, 5685–5689. European Microbiological Societies Microbial
Ecology 89, 490-494.

228 | Perdigonet al.

 J. Bio. Env. Sci. 2016

Greening C, Carerec CR, Rushton-Greena R, of soil and flora composition in the Atlantic
Harolda LK, Hardsa K,Taylor MC, Morales rainforest. PLOS ONE 11,1-19.
SE, Stott MB, Cook GM. 2015. Persistence of the
dominant soil phylum Acidobacteria by trace gas McLaughlin DJ, Hibbett DS, Lutzoni F,
scavenging. Proceedings of the National Academy of Spatafora JW, Vilgalys R. 2009. The search for
Sciences 112, 10497–10502. the fungal tree of life. Trends in Microbiology 17,
488-497.
Hill TCJ, Walsh KA, Harris JA, Moffett BF.
2003. Using ecological diversity measures with Nannipieri P, Ascher J, Ceccherini MT, Landi
bacterial communities. Federation of European L, Pietramellara G, Renella G. 2003. Microbial
Microbiological Societies Microbiology Ecology 43, diversity and soil functions. European Journal of Soil
1–11. Science54,655–670.

Janssen PH. 2006. Identifying the dominant soil Nicol GW, Leininger S, Schleper C, ProsserJI.
bacterial taxa in libraries of 16S rRNA and 16S rRNA 2008. The influence of soil pH on the diversity,
genes. Applied and Environmental Microbiology 72, abundance and transcriptional activity of ammonia
1719–1728. oxidizing archaea and bacteria. Environmental
Microbiology 10, 2966–2978.
Kirk JL, Beaudette LA, Hart M, Moutoglis P,
Klironomos JN, Lee H, Trevors JT. 2004. Reysenbach AL, Wickham G, Pace N. 1994.
Methods of studying soil microbial diversity. Journal Phylogenetic analysis of the hyperthermophilic pink
of Microbiological Methods 58, 169–188. filament community in Octopus Spring, Yellowstone
National Park. Applied and Environmental
Kowalchuk GA, Stephen JA. 2001. Ammonia- Microbiology 60, 2113–2119.
oxidizing bacteria: a model for molecular microbial
ecology. Annual Review of Microbiology55, 485–529. Saitou N, Nei M.1987. The neighbor-joining
method: A new method for reconstructing
Lane DJ. 1991. 16S/23S rRNA sequencing. In phylogenetic trees. Molecular Biology and
Stackebrandt E, Goodfellow M, Ed. Nucleic acid Evolution4, 406-425.
techniques in bacterial systematics. John Wiley &
Sons, Ltd. Chichester, England, 115–175. Santos EC, Armas ED, Crowley D, Lambais
MR. 2014. Artificial neural network modeling of
Lladó S, Benada O, Cajthaml T, Baldrian microbial community structures in the Atlantic Forest
P, García-Fraile P. 2015. Silvibacterium of Brazil. Soil Biol Biochem 69, 101–109.
bohemicum gen. nov. sp. nov., an acidobacterium
isolated from coniferous soil in the Bohemian Forest Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X.
National Park. Systematic and Applied 2013. Soil pH drives the spatial distribution of
Microbiology39, 14-19. bacterial communities along elevation on Changbai
mountain. Soil Biology and Biochemistry 57, 204–
Lima-Perim JE, Romagnoli EM, Dini- 211.
Andreote F, Durrer A, Cavalcante A, Dias F,
Dini Andreote F. 2016. Linking the composition of Siles JA, Cajthaml T, Minerbi S, Margesin R.
bacterial and Archaeal communities to characteristics 2016. Effect of altitude and season on microbial
activity, abundance and community structure in

229 | Perdigonet al.


Alpine forest soils. Federation of European
Microbiological Societies Microbial Ecology92.
Singh D, Takahashi K, Kim M, Chun J, Adams
JM. 2012. A hump-backed trend in bacterial diversity
with elevation on Mount Fuji, Japan. Microbial
Ecology 63, 429-37.
Stackebrandt E, Liesack W. 1993. Nucleic acids
and classification. In Goodfellow M, O’Donnell AG,
Eds. Handbook of New Bacterial Systematics.
Academic Press, London. 152–189.
Trasar-Cepeda C, Leiros C, Gil-Sotres F,
Seoane S. 1998. Towards a biochemical quality
index for soils: An expression relating several
biological and biochemical properties. Biology and
Fertility of Soils26, 100-106.
Tripathi BM, Kim M, Singh D, Lee-Cruz L, Lai-
Hoe A, Ainuddin AN, Go R, Abdul Rahim R,
Husni MHA, Chun J, Adams JM. 2012. Tropical
soil bacterial communities in Malaysia: pH dominates
in the equatorial tropics too. Microbial Ecology 64,
474–484.
230 | Perdigonet al.
J. Bio. Env. Sci. 2016
Tripathi BM, Kim M, Lai-Hoe A, Shukor NA,
Rahim RA, Go R, Adams, JM. 2013. pH
dominates variation in tropical soil archaeal diversity
and community structure. Federation of European
Microbiological Societies Microbial Ecology 86, 303–
311.
Tamura K, Stecher G, Peterson D. Filipski A,
Kumar S. 2013. MEGA6: Molecular Evolutionary
Genetics Analysis Version 6.0. Molecular Biology and
Evolution 30, 2725- 2729.
Whitman WB, Coleman DC, Wiebe WJ. 1998.
Prokaryotes: The unseen majority. Proceedings
National Academy of Science USA95, 6578–6583.
Zhang LM, Wang M, Prosser JI, Zheng YM, He
JZ. 2009. Altitude ammonia-oxidizing bacteria and
archaea in soils of Mount Everest. Federation of
European Microbiological Societies Microbiology
Ecology 70, 208–217.
Zhang CL, Xie W, Martin-Cuadrado
AB, Rodriguez-Valera F. 2015. Marine Group
II Archaea, potentially important players in the global
ocean carbon cycle. Frontiers in Microbiology6,1-9.